Database accession: MF7000617
Name: MarR familz protein, Sco5413 (Streptomyces coelicolor)
PDB ID: 4b8x
Experimental method: X-ray (1.25 Å)
Assembly: Homodimer
Source organism: Streptomyces coelicolor
Primary publication of the structure:
Holley TA, Stevenson CE, Bibb MJ, Lawson DM
High resolution crystal structure of Sco5413, a widespread actinomycete MarR family transcriptional regulator of unknown function.
(2013) Proteins 81: 176-82
PMID: 23042442
Abstract:
The crystal structure of Sco5413 from Streptomyces coelicolor A3(2) has been determined at 1.25 Å resolution, the highest resolution reported for a MarR family transcriptional regulator. Putative orthologs are encoded by the majority of sequenced actinomycete genomes, and may play roles in regulating growth and antibiotic production, but they have yet to be assigned a precise function. Sco5413 forms a homodimer and, through comparisons with other MarR family protein structures, we postulate that it adopts a conformation compatible with DNA binding, and that a channel at the dimer interface, lined by well-conserved residues, is the binding site of an unidentified effector ligand.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
DNA binding DNA binding
DNA-binding transcription factor activity DNA-binding transcription factor activity
Biological process:
regulation of DNA-templated transcription regulation of DNA-templated transcription
response to stress response to stress
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Possible MarR-transcriptional regulator
Source organism: Streptomyces coelicolor
Length: 169 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPKPLSLSFDPIARADELWAQRWGGVPSMAAITSIMRAQQILLGEVDAVVKPYGLTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEAATRDLMAMDFGLGAYDAEECGEIFAMLRPLRVAAGDFDED
UniProtKB AC: Q9L2A7 (positions: 25-168)
Coverage: 85%
Name: Possible MarR-transcriptional regulator
Source organism: Streptomyces coelicolor
Length: 169 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPKPLSLSFDPIARADELWAQRWGGVPSMAAITSIMRAQQILLGEVDAVVKPYGLTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEAATRDLMAMDFGLGAYDAEECGEIFAMLRPLRVAAGDFDED
UniProtKB AC: Q9L2A7 (positions: 25-168)
Coverage: 85%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Winged helix DNA-binding domain (MarR type I) transcriptional regulator
Evidence level: Direct evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The MarR-type family transcriptional regulator, NadR is dimeric in solution (SE-HPLC/MALLS) as other MarR faimily proteins (PMID:18272181). Compared to ligand-stabilized holo-NadR, apo-NadR displayed an intrinsic flexibility focused in the DNA-binding region (PMID:27105075). The structural features of several family members have been described, they all have two subdomains: there is a helix-turn-helix (HTH) DNA-binding domain plus dimerization helices that form an interlocked dimerization domain. Dimerization is mediated by helices α1, α5, and α6 from each monomer resulting in an interlocked, tight dimer burying a large, hydrophobic solvent-accessible surface area. The structure of the dimerization region reveals domain swapping, where α1 of one subunit is inserted between α5′ and α6′ of the other subunit and forms a coiled coil with helix α6′ (PMID:19586910). The DNA-binding elements contain helices α3-α4 and strands β1-β2 from each monomer (PMID:29794028, PMID:35367827).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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